Author: mes Date: 2012-04-06 14:21:05 -0700 (Fri, 06 Apr 2012) New Revision: 28757
Added: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBFilter.java csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java Removed: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPFilter.java csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold csplugins/trunk/ucsd/mes/genomespace/gxp-reader/ Modified: csplugins/trunk/ucsd/mes/genomespace/pom.xml Log: more renaming Deleted: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml 2012-04-06 21:01:19 UTC (rev 28754) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml 2012-04-06 21:21:05 UTC (rev 28757) @@ -1,113 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> - <modelVersion>4.0.0</modelVersion> - - <parent> - <artifactId>genomespace-parent</artifactId> - <groupId>cytoscape</groupId> - <version>1.0-SNAPSHOT</version> - </parent> - - <groupId>cytoscape</groupId> - <artifactId>gxp-reader</artifactId> - <packaging>jar</packaging> - <name>GXP Reader Plugin</name> - - <build> - <plugins> - <plugin> - <groupId>org.apache.maven.plugins</groupId> - <artifactId>maven-compiler-plugin</artifactId> - <version>2.3.2</version> - <configuration> - <source>1.6</source> - <target>1.6</target> - <optimize>true</optimize> - <showWarnings>true</showWarnings> - <showDeprecation>true</showDeprecation> - </configuration> - </plugin> - <plugin> - <artifactId>maven-assembly-plugin</artifactId> - <version>2.2-beta-5</version> - <configuration> - <archive> - <manifestEntries> - <Cytoscape-Plugin>cytoscape.gxp.GXPReaderPlugin</Cytoscape-Plugin> - </manifestEntries> - </archive> - <descriptors> - <descriptor>src/main/assembly/src.xml</descriptor> - </descriptors> - </configuration> - <executions> - <execution> - <id>make-assembly</id> - <phase>package</phase> - <goals> - <goal>single</goal> - </goals> - </execution> - </executions> - </plugin> - </plugins> - </build> - - <dependencies> - <dependency> - <groupId>cytoscape</groupId> - <artifactId>application</artifactId> - <version>2.8.3-SNAPSHOT</version> - <scope>provided</scope> - </dependency> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>3.8.1</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.jdom</groupId> - <artifactId>jdom</artifactId> - <version>1.1</version> - <scope>provided</scope> - </dependency> - </dependencies> - - <repositories> - <repository> - <id>cytoscape_snapshots</id> - <snapshots> - <enabled>true</enabled> - </snapshots> - <releases> - <enabled>false</enabled> - </releases> - <name>Cytoscape Snapshots</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> - </repository> - <repository> - <id>cytoscape_releases</id> - <snapshots> - <enabled>false</enabled> - </snapshots> - <releases> - <enabled>true</enabled> - </releases> - <name>Cytoscape Releases</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> - </repository> - <repository> - <id>cytoscape_thirdparty</id> - <snapshots> - <enabled>false</enabled> - </snapshots> - <releases> - <enabled>true</enabled> - </releases> - <name>Cytoscape Third Party</name> - <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> - </repository> - </repositories> - -</project> Copied: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml (from rev 28756, csplugins/trunk/ucsd/mes/genomespace/gxp-reader/pom.xml) =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/pom.xml 2012-04-06 21:21:05 UTC (rev 28757) @@ -0,0 +1,113 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> + <modelVersion>4.0.0</modelVersion> + + <parent> + <artifactId>genomespace-parent</artifactId> + <groupId>cytoscape</groupId> + <version>1.0-SNAPSHOT</version> + </parent> + + <groupId>cytoscape</groupId> + <artifactId>cdb-reader</artifactId> + <packaging>jar</packaging> + <name>CDB Reader Plugin</name> + + <build> + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-compiler-plugin</artifactId> + <version>2.3.2</version> + <configuration> + <source>1.6</source> + <target>1.6</target> + <optimize>true</optimize> + <showWarnings>true</showWarnings> + <showDeprecation>true</showDeprecation> + </configuration> + </plugin> + <plugin> + <artifactId>maven-assembly-plugin</artifactId> + <version>2.2-beta-5</version> + <configuration> + <archive> + <manifestEntries> + <Cytoscape-Plugin>cytoscape.gxp.CDBReaderPlugin</Cytoscape-Plugin> + </manifestEntries> + </archive> + <descriptors> + <descriptor>src/main/assembly/src.xml</descriptor> + </descriptors> + </configuration> + <executions> + <execution> + <id>make-assembly</id> + <phase>package</phase> + <goals> + <goal>single</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>cytoscape</groupId> + <artifactId>application</artifactId> + <version>2.8.3-SNAPSHOT</version> + <scope>provided</scope> + </dependency> + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <version>3.8.1</version> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.jdom</groupId> + <artifactId>jdom</artifactId> + <version>1.1</version> + <scope>provided</scope> + </dependency> + </dependencies> + + <repositories> + <repository> + <id>cytoscape_snapshots</id> + <snapshots> + <enabled>true</enabled> + </snapshots> + <releases> + <enabled>false</enabled> + </releases> + <name>Cytoscape Snapshots</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url> + </repository> + <repository> + <id>cytoscape_releases</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Releases</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url> + </repository> + <repository> + <id>cytoscape_thirdparty</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Third Party</name> + <url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url> + </repository> + </repositories> + +</project> Copied: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBFilter.java (from rev 28756, csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBFilter.java) =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBFilter.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBFilter.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -0,0 +1,81 @@ + +/* + Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) + + The Cytoscape Consortium is: + - Institute for Systems Biology + - University of California San Diego + - Memorial Sloan-Kettering Cancer Center + - Institut Pasteur + - Agilent Technologies + + This library is free software; you can redistribute it and/or modify it + under the terms of the GNU Lesser General Public License as published + by the Free Software Foundation; either version 2.1 of the License, or + any later version. + + This library is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF + MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and + documentation provided hereunder is on an "as is" basis, and the + Institute for Systems Biology and the Whitehead Institute + have no obligations to provide maintenance, support, + updates, enhancements or modifications. In no event shall the + Institute for Systems Biology and the Whitehead Institute + be liable to any party for direct, indirect, special, + incidental or consequential damages, including lost profits, arising + out of the use of this software and its documentation, even if the + Institute for Systems Biology and the Whitehead Institute + have been advised of the possibility of such damage. See + the GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with this library; if not, write to the Free Software Foundation, + Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. +*/ + +package cytoscape.gxp; + +import cytoscape.data.ImportHandler; + +import cytoscape.data.readers.GraphReader; + +import cytoscape.util.CyFileFilter; + +import java.io.File; +import java.io.IOException; + + +public class CDBFilter extends CyFileFilter { + /** + * CDB Files are Graphs. + */ + private static String fileNature = ImportHandler.GRAPH_NATURE; + + /** + * File Extensions. + */ + private static String[] fileExtensions = { "cdb" }; + + /** + * Filter Description. + */ + private static String description = "CDB files"; + + /** + * Constructor. + */ + public CDBFilter() { + super(fileExtensions, description, fileNature); + } + + /** + * Gets the appropirate GraphReader object. + * + * @param fileName File Name. + * @return GraphReader Object. + */ + public GraphReader getReader(String fileName) { + return new CDBGraphReader(fileName); + } +} Copied: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java (from rev 28756, csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java) =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBGraphReader.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -0,0 +1,211 @@ + +/* + Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) + + The Cytoscape Consortium is: + - Institute for Systems Biology + - University of California San Diego + - Memorial Sloan-Kettering Cancer Center + - Institut Pasteur + - Agilent Technologies + + This library is free software; you can redistribute it and/or modify it + under the terms of the GNU Lesser General Public License as published + by the Free Software Foundation; either version 2.1 of the License, or + any later version. + + This library is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF + MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and + documentation provided hereunder is on an "as is" basis, and the + Institute for Systems Biology and the Whitehead Institute + have no obligations to provide maintenance, support, + updates, enhancements or modifications. In no event shall the + Institute for Systems Biology and the Whitehead Institute + be liable to any party for direct, indirect, special, + incidental or consequential damages, including lost profits, arising + out of the use of this software and its documentation, even if the + Institute for Systems Biology and the Whitehead Institute + have been advised of the possibility of such damage. See + the GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with this library; if not, write to the Free Software Foundation, + Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. +*/ + +package cytoscape.gxp; + +import cytoscape.CyEdge; +import cytoscape.CyNetwork; +import cytoscape.CyNode; +import cytoscape.Cytoscape; + +import cytoscape.data.CyAttributes; +import cytoscape.data.Semantics; + +import org.jdom.Document; +import org.jdom.Element; +import org.jdom.JDOMException; + +import org.jdom.input.SAXBuilder; + + +import cytoscape.data.readers.AbstractGraphReader; +import cytoscape.data.readers.GraphReader; + +import cytoscape.view.CyNetworkView; +import cytoscape.view.CytoscapeDesktop; + +import cytoscape.visual.*; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; + +import java.net.URL; + +import java.util.*; + + +/** + * @author Mike Smoot + */ +public class CDBGraphReader extends AbstractGraphReader implements GraphReader { + // node id from file -> node + private Map<String,CyNode> geneIdMap; + + private List<Integer> nodeIds; + private List<Integer> edgeIds; + private URL fileURL; + + /** + * Creates a new SBMLGraphReader object. + * + * @param filename DOCUMENT ME! + */ + public CDBGraphReader(String filename) { + super(filename); + fileURL = null; + } + + /** + * Creates a new SBMLGraphReader object. + * + * @param url DOCUMENT ME! + */ + public CDBGraphReader(URL url) { + super(null); + fileURL = url; + fileName = null; + } + + /** + * DOCUMENT ME! + * + * @throws IOException DOCUMENT ME! + */ + public void read() throws IOException { + InputStream instream; + + if ((fileURL == null) && (fileName != null)) + instream = new FileInputStream(fileName); + else if ((fileURL != null) && (fileName == null)) + instream = fileURL.openStream(); + else + throw new IOException("No file to open!"); + + nodeIds = new ArrayList<Integer>(); + edgeIds = new ArrayList<Integer>(); + + geneIdMap = new HashMap<String,CyNode>(); + + try { + + // Actual work + SAXBuilder builder = new SAXBuilder(false); + Document doc = builder.build(instream); + + createGeneNodes( getTable(doc,"Genes") ); + createRegulatorsRegulatorsEdges( getTable(doc,"Regulators_Regulators") ); + + } catch (JDOMException je) { + throw new IOException("JDOM failure parsing file.",je); + } + } + + private void createRegulatorsRegulatorsEdges(Element regulatorsRegulators) { + for ( Object o : regulatorsRegulators.getChildren("Regulator_Gene") ) { + Element regulatorGene = (Element)o; + String regulatorId = regulatorGene.getAttributeValue("Regulator_Id"); + String geneId = regulatorGene.getAttributeValue("Gene_Id"); + if ( regulatorId == null || + geneId == null || + !geneIdMap.containsKey(regulatorId) || + !geneIdMap.containsKey(geneId) ) + continue; + + CyNode na = geneIdMap.get(regulatorId); + CyNode nb = geneIdMap.get(geneId); + CyEdge e = Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true); + edgeIds.add( e.getRootGraphIndex() ); + } + } + + + private void createGeneNodes(Element genes) { + for ( Object o : genes.getChildren("Gene") ) { + Element gene = (Element) o; + CyNode node = Cytoscape.getCyNode(gene.getAttributeValue("ORF"),true); + String id = gene.getAttributeValue("Id"); + geneIdMap.put(id,node); + nodeIds.add( node.getRootGraphIndex() ); + } + } + + private Element getTable(Document doc, String tableName) { + for ( Object e : doc.getRootElement().getChildren("Table") ) + if ( tableName.equals(((Element)e).getAttributeValue("Type")) ) + return (Element)e; + + return null; + } + + public void doPostProcessing(CyNetwork network) { + /* + // Set SBML specific visual style + VisualMappingManager manager = Cytoscape.getVisualMappingManager(); + CalculatorCatalog catalog = manager.getCalculatorCatalog(); + + VisualStyle vs = catalog.getVisualStyle(SBMLVisualStyleFactory.SBMLReader_VS); + + if (vs == null) { + vs = SBMLVisualStyleFactory.createVisualStyle(network); + catalog.addVisualStyle(vs); + } + + manager.setVisualStyle(vs); + Cytoscape.getCurrentNetworkView().setVisualStyle(vs.getName()); + Cytoscape.getCurrentNetworkView().applyVizmapper(vs); + */ + } + + public int[] getNodeIndicesArray() { + int[] nodes = new int[nodeIds.size()]; + + for (int i = 0; i < nodes.length; i++) + nodes[i] = nodeIds.get(i).intValue(); + + return nodes; + } + + public int[] getEdgeIndicesArray() { + int[] edges = new int[edgeIds.size()]; + + for (int i = 0; i < edges.length; i++) + edges[i] = edgeIds.get(i).intValue(); + + return edges; + } +} Copied: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java (from rev 28756, csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java) =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java (rev 0) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/CDBReaderPlugin.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -0,0 +1,23 @@ +package cytoscape.gxp; + +import cytoscape.Cytoscape; +import cytoscape.data.ImportHandler; +import cytoscape.plugin.CytoscapePlugin; + + +/** + * This class is used to instantiate your plugin. Put whatever initialization code + * you need into the no argument constructor (the only one that will be called). + * The actual functionality of your plugin can be in this class, but should + * probably be separated into separted classes that get instantiated here. + */ +public class CDBReaderPlugin extends CytoscapePlugin { + + public CDBReaderPlugin() { + super(); + ImportHandler ih = Cytoscape.getImportHandler(); + ih.addFilter(new CDBFilter()); + } +} + + Deleted: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPFilter.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPFilter.java 2012-04-06 21:01:19 UTC (rev 28754) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPFilter.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -1,81 +0,0 @@ - -/* - Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) - - The Cytoscape Consortium is: - - Institute for Systems Biology - - University of California San Diego - - Memorial Sloan-Kettering Cancer Center - - Institut Pasteur - - Agilent Technologies - - This library is free software; you can redistribute it and/or modify it - under the terms of the GNU Lesser General Public License as published - by the Free Software Foundation; either version 2.1 of the License, or - any later version. - - This library is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF - MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and - documentation provided hereunder is on an "as is" basis, and the - Institute for Systems Biology and the Whitehead Institute - have no obligations to provide maintenance, support, - updates, enhancements or modifications. In no event shall the - Institute for Systems Biology and the Whitehead Institute - be liable to any party for direct, indirect, special, - incidental or consequential damages, including lost profits, arising - out of the use of this software and its documentation, even if the - Institute for Systems Biology and the Whitehead Institute - have been advised of the possibility of such damage. See - the GNU Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public License - along with this library; if not, write to the Free Software Foundation, - Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. -*/ - -package cytoscape.gxp; - -import cytoscape.data.ImportHandler; - -import cytoscape.data.readers.GraphReader; - -import cytoscape.util.CyFileFilter; - -import java.io.File; -import java.io.IOException; - - -public class GXPFilter extends CyFileFilter { - /** - * GXP Files are Graphs. - */ - private static String fileNature = ImportHandler.GRAPH_NATURE; - - /** - * File Extensions. - */ - private static String[] fileExtensions = { "gxp" }; - - /** - * Filter Description. - */ - private static String description = "GXP files"; - - /** - * Constructor. - */ - public GXPFilter() { - super(fileExtensions, description, fileNature); - } - - /** - * Gets the appropirate GraphReader object. - * - * @param fileName File Name. - * @return GraphReader Object. - */ - public GraphReader getReader(String fileName) { - return new GXPGraphReader(fileName); - } -} Deleted: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java 2012-04-06 21:01:19 UTC (rev 28754) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -1,211 +0,0 @@ - -/* - Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) - - The Cytoscape Consortium is: - - Institute for Systems Biology - - University of California San Diego - - Memorial Sloan-Kettering Cancer Center - - Institut Pasteur - - Agilent Technologies - - This library is free software; you can redistribute it and/or modify it - under the terms of the GNU Lesser General Public License as published - by the Free Software Foundation; either version 2.1 of the License, or - any later version. - - This library is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF - MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and - documentation provided hereunder is on an "as is" basis, and the - Institute for Systems Biology and the Whitehead Institute - have no obligations to provide maintenance, support, - updates, enhancements or modifications. In no event shall the - Institute for Systems Biology and the Whitehead Institute - be liable to any party for direct, indirect, special, - incidental or consequential damages, including lost profits, arising - out of the use of this software and its documentation, even if the - Institute for Systems Biology and the Whitehead Institute - have been advised of the possibility of such damage. See - the GNU Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public License - along with this library; if not, write to the Free Software Foundation, - Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. -*/ - -package cytoscape.gxp; - -import cytoscape.CyEdge; -import cytoscape.CyNetwork; -import cytoscape.CyNode; -import cytoscape.Cytoscape; - -import cytoscape.data.CyAttributes; -import cytoscape.data.Semantics; - -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; - -import org.jdom.input.SAXBuilder; - - -import cytoscape.data.readers.AbstractGraphReader; -import cytoscape.data.readers.GraphReader; - -import cytoscape.view.CyNetworkView; -import cytoscape.view.CytoscapeDesktop; - -import cytoscape.visual.*; - -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; - -import java.net.URL; - -import java.util.*; - - -/** - * @author Mike Smoot - */ -public class GXPGraphReader extends AbstractGraphReader implements GraphReader { - // node id from file -> node - private Map<String,CyNode> geneIdMap; - - private List<Integer> nodeIds; - private List<Integer> edgeIds; - private URL fileURL; - - /** - * Creates a new SBMLGraphReader object. - * - * @param filename DOCUMENT ME! - */ - public GXPGraphReader(String filename) { - super(filename); - fileURL = null; - } - - /** - * Creates a new SBMLGraphReader object. - * - * @param url DOCUMENT ME! - */ - public GXPGraphReader(URL url) { - super(null); - fileURL = url; - fileName = null; - } - - /** - * DOCUMENT ME! - * - * @throws IOException DOCUMENT ME! - */ - public void read() throws IOException { - InputStream instream; - - if ((fileURL == null) && (fileName != null)) - instream = new FileInputStream(fileName); - else if ((fileURL != null) && (fileName == null)) - instream = fileURL.openStream(); - else - throw new IOException("No file to open!"); - - nodeIds = new ArrayList<Integer>(); - edgeIds = new ArrayList<Integer>(); - - geneIdMap = new HashMap<String,CyNode>(); - - try { - - // Actual work - SAXBuilder builder = new SAXBuilder(false); - Document doc = builder.build(instream); - - createGeneNodes( getTable(doc,"Genes") ); - createRegulatorsRegulatorsEdges( getTable(doc,"Regulators_Regulators") ); - - } catch (JDOMException je) { - throw new IOException("JDOM failure parsing file.",je); - } - } - - private void createRegulatorsRegulatorsEdges(Element regulatorsRegulators) { - for ( Object o : regulatorsRegulators.getChildren("Regulator_Gene") ) { - Element regulatorGene = (Element)o; - String regulatorId = regulatorGene.getAttributeValue("Regulator_Id"); - String geneId = regulatorGene.getAttributeValue("Gene_Id"); - if ( regulatorId == null || - geneId == null || - !geneIdMap.containsKey(regulatorId) || - !geneIdMap.containsKey(geneId) ) - continue; - - CyNode na = geneIdMap.get(regulatorId); - CyNode nb = geneIdMap.get(geneId); - CyEdge e = Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true); - edgeIds.add( e.getRootGraphIndex() ); - } - } - - - private void createGeneNodes(Element genes) { - for ( Object o : genes.getChildren("Gene") ) { - Element gene = (Element) o; - CyNode node = Cytoscape.getCyNode(gene.getAttributeValue("ORF"),true); - String id = gene.getAttributeValue("Id"); - geneIdMap.put(id,node); - nodeIds.add( node.getRootGraphIndex() ); - } - } - - private Element getTable(Document doc, String tableName) { - for ( Object e : doc.getRootElement().getChildren("Table") ) - if ( tableName.equals(((Element)e).getAttributeValue("Type")) ) - return (Element)e; - - return null; - } - - public void doPostProcessing(CyNetwork network) { - /* - // Set SBML specific visual style - VisualMappingManager manager = Cytoscape.getVisualMappingManager(); - CalculatorCatalog catalog = manager.getCalculatorCatalog(); - - VisualStyle vs = catalog.getVisualStyle(SBMLVisualStyleFactory.SBMLReader_VS); - - if (vs == null) { - vs = SBMLVisualStyleFactory.createVisualStyle(network); - catalog.addVisualStyle(vs); - } - - manager.setVisualStyle(vs); - Cytoscape.getCurrentNetworkView().setVisualStyle(vs.getName()); - Cytoscape.getCurrentNetworkView().applyVizmapper(vs); - */ - } - - public int[] getNodeIndicesArray() { - int[] nodes = new int[nodeIds.size()]; - - for (int i = 0; i < nodes.length; i++) - nodes[i] = nodeIds.get(i).intValue(); - - return nodes; - } - - public int[] getEdgeIndicesArray() { - int[] edges = new int[edgeIds.size()]; - - for (int i = 0; i < edges.length; i++) - edges[i] = edgeIds.get(i).intValue(); - - return edges; - } -} Deleted: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java 2012-04-06 21:01:19 UTC (rev 28754) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/GXPReaderPlugin.java 2012-04-06 21:21:05 UTC (rev 28757) @@ -1,23 +0,0 @@ -package cytoscape.gxp; - -import cytoscape.Cytoscape; -import cytoscape.data.ImportHandler; -import cytoscape.plugin.CytoscapePlugin; - - -/** - * This class is used to instantiate your plugin. Put whatever initialization code - * you need into the no argument constructor (the only one that will be called). - * The actual functionality of your plugin can be in this class, but should - * probably be separated into separted classes that get instantiated here. - */ -public class GXPReaderPlugin extends CytoscapePlugin { - - public GXPReaderPlugin() { - super(); - ImportHandler ih = Cytoscape.getImportHandler(); - ih.addFilter(new GXPFilter()); - } -} - - Deleted: csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/gxp-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold 2012-04-06 21:01:19 UTC (rev 28754) +++ csplugins/trunk/ucsd/mes/genomespace/cdb-reader/src/main/java/cytoscape/gxp/SBMLVisualStyleFactory.java.hold 2012-04-06 21:21:05 UTC (rev 28757) @@ -1,165 +0,0 @@ - -/* - Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) - - The Cytoscape Consortium is: - - Institute for Systems Biology - - University of California San Diego - - Memorial Sloan-Kettering Cancer Center - - Institut Pasteur - - Agilent Technologies - - This library is free software; you can redistribute it and/or modify it - under the terms of the GNU Lesser General Public License as published - by the Free Software Foundation; either version 2.1 of the License, or - any later version. - - This library is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF - MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and - documentation provided hereunder is on an "as is" basis, and the - Institute for Systems Biology and the Whitehead Institute - have no obligations to provide maintenance, support, - updates, enhancements or modifications. In no event shall the - Institute for Systems Biology and the Whitehead Institute - be liable to any party for direct, indirect, special, - incidental or consequential damages, including lost profits, arising - out of the use of this software and its documentation, even if the - Institute for Systems Biology and the Whitehead Institute - have been advised of the possibility of such damage. See - the GNU Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public License - along with this library; if not, write to the Free Software Foundation, - Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. -*/ - -package sbmlreader; - -import cytoscape.*; - -import cytoscape.data.Semantics; - -import cytoscape.view.CytoscapeDesktop; - -import cytoscape.visual.*; - -import cytoscape.visual.calculators.*; - -import cytoscape.visual.mappings.*; - -import cytoscape.visual.ui.*; - -import giny.view.EdgeView; - -import java.awt.Color; - - -/** - * VisualStyleFactory.java - * This class defines the visualstyle in Cytoscape for the SBMLReader plugin. - * - * @author W.P.A. Ligtenberg, Eindhoven University of Technology - */ -public class SBMLVisualStyleFactory { - /** - * - */ - public static final String SBMLReader_VS = "SBMLReader Style"; - - /** - * - */ - public static final String NODE_TYPE_ATT = "sbml type"; - - /** - * - */ - public static final String EDGE_TYPE_ATT = "interaction"; - - /** - * DOCUMENT ME! - * - * @param network DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static VisualStyle createVisualStyle(CyNetwork network) { - VisualMappingManager vmManager = Cytoscape.getVisualMappingManager(); - NodeAppearanceCalculator nodeAppCalc = new NodeAppearanceCalculator(); - EdgeAppearanceCalculator edgeAppCalc = new EdgeAppearanceCalculator(); - CalculatorCatalog calculatorCatalog = vmManager.getCalculatorCatalog(); - - // ------------------------------ Set node shapes ---------------------------// - DiscreteMapping disMapping = new DiscreteMapping(NodeShape.RECT, - ObjectMapping.NODE_MAPPING); - disMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false); - disMapping.putMapValue("species", NodeShape.DIAMOND); - disMapping.putMapValue("reaction", NodeShape.ELLIPSE); - - Calculator shapeCalculator = new BasicCalculator("SBMLReader Shape Calculator", - disMapping, - VisualPropertyType.NODE_SHAPE); - nodeAppCalc.setCalculator(shapeCalculator); - - // ------------------------------ Set the label ------------------------------// - // Display the value for geneName as a label - String cName = "sbml name"; - Calculator nlc = calculatorCatalog.getCalculator(VisualPropertyType.NODE_LABEL, cName); - - if (nlc == null) { - PassThroughMapping m = new PassThroughMapping(new String(), cName); - nlc = new BasicCalculator(cName, m, VisualPropertyType.NODE_LABEL); - } - - nodeAppCalc.setCalculator(nlc); - - //--------------------- Set the size of the nodes --------------------------// - //Discrete mapping on nodeType - Double speciesNodeSize = new Double(30); - Double reactionNodeSize = new Double(30); - DiscreteMapping sizeMapping = new DiscreteMapping(reactionNodeSize, - ObjectMapping.NODE_MAPPING); - sizeMapping.setControllingAttributeName(NODE_TYPE_ATT, network, false); - sizeMapping.putMapValue("species", speciesNodeSize); - sizeMapping.putMapValue("reaction", reactionNodeSize); - - Calculator sizeCalculator = new BasicCalculator("SBMLReader Size Calculator", - sizeMapping, - VisualPropertyType.NODE_SIZE); - nodeAppCalc.setCalculator(sizeCalculator); - nodeAppCalc.setNodeSizeLocked(true); - - // ------------------------------ Set edge arrow shape ---------------------------// - DiscreteMapping arrowMapping = new DiscreteMapping(ArrowShape.DELTA, - ObjectMapping.NODE_MAPPING); - arrowMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false); - arrowMapping.putMapValue("reaction-product", ArrowShape.ARROW); - arrowMapping.putMapValue("reaction-reactant", ArrowShape.NONE); - arrowMapping.putMapValue("reaction-modifier", ArrowShape.CIRCLE); - - Calculator edgeArrowCalculator = new BasicCalculator("SBMLReader Edge Arrow Calculator", - arrowMapping, - VisualPropertyType.EDGE_SRCARROW_SHAPE); - edgeAppCalc.setCalculator(edgeArrowCalculator); - - // ------------------------------ Set edge colour ---------------------------// - DiscreteMapping edgeColorMapping = new DiscreteMapping(Color.BLACK, - ObjectMapping.NODE_MAPPING); - edgeColorMapping.setControllingAttributeName(EDGE_TYPE_ATT, network, false); - edgeColorMapping.putMapValue("reaction-product", Color.GREEN); - edgeColorMapping.putMapValue("reaction-reactant", Color.RED); - edgeColorMapping.putMapValue("reaction-modifier", Color.BLACK); - - Calculator edgeColorCalculator = new BasicCalculator("SBMLReader Edge Color Calculator", - edgeColorMapping, - VisualPropertyType.EDGE_COLOR); - edgeAppCalc.setCalculator(edgeColorCalculator); - - //------------------------- Create a visual style -------------------------------// - GlobalAppearanceCalculator gac = vmManager.getVisualStyle().getGlobalAppearanceCalculator(); - VisualStyle visualStyle = new VisualStyle(SBMLReader_VS, nodeAppCalc, edgeAppCalc, gac); - - return visualStyle; - } -} Modified: csplugins/trunk/ucsd/mes/genomespace/pom.xml =================================================================== --- csplugins/trunk/ucsd/mes/genomespace/pom.xml 2012-04-06 21:19:10 UTC (rev 28756) +++ csplugins/trunk/ucsd/mes/genomespace/pom.xml 2012-04-06 21:21:05 UTC (rev 28757) @@ -11,7 +11,7 @@ <modules> <module>genomespace-libs-plugin</module> <module>genomespace-plugin</module> - <module>gxp-reader</module> + <module>cdb-reader</module> <module>cytable-reader</module> <!-- webstart actually has a different parent (cytoscape-webstart) so we don't include it here! It needs to be built separately. -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/cytoscape-cvs?hl=en.
